


On the Motions of Atoms

by guardingdark



Category: Doctor Who (1963), Doctor Who (2005), Doctor Who: Eighth Doctor Adventures - Various Authors, Sarah Jane Adventures
Genre: Alien Cultural Differences, Alternate Universe - Canon Divergence, Developing Relationship, Dr Nyarlathotep | Time Lords Are Aliens, F/F, F/M, Hurt Barely Any Comfort, M/M, Other, Psychological Trauma, Year That Never Was
Language: English
Status: In-Progress
Published: 2016-06-09
Updated: 2016-06-09
Packaged: 2018-06-10 04:51:25
Rating: Mature
Warnings: Graphic Depictions Of Violence, Major Character Death, Rape/Non-Con
Chapters: 1
Words: 3,565
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/6940573
Author URL: https://archiveofourown.org/users/guardingdark/pseuds/guardingdark
Summary: <blockquote class="userstuff">
              <p>The Master's taken over the Earth and the Doctor may not have thought through this whole "make everyone believe I can save them" plan very well.</p>
            </blockquote>





	On the Motions of Atoms

**Author's Note:**

  * Inspired by [And All the Wandering Motions](https://archiveofourown.org/works/1038770) by [guardingdark](https://archiveofourown.org/users/guardingdark/pseuds/guardingdark), [mylordshesacactus](https://archiveofourown.org/users/mylordshesacactus/pseuds/mylordshesacactus). 



> This is a triggerfic; **if it's tagged, it's a major theme**. Stay safe.
> 
> PLEASE NOTE: this chapter contains depictions of and/or references to **body horror, death, dehumanizing language, domestic abuse, fantastic racism/xenophobia, genocide, molestation, sex, torture, and trypophobia.**

In retrospect, Jack Harkness thought, it had been kind of a shitty plan.

He fingered the _Tardis_ key around his neck as he moved to avoid a cameraman, and he tried to think about fingering _other_ things instead of about how screwed they all were when this whole mess inevitably went to hell.

At least the Doctor had been right that the low-level perception filter built into what looked like a plain old Yale key you'd see on any keychain, but at the touch was this weird sort of semicircle with triangle imprints, would work to fool anybody who wasn't looking too hard that they weren't there. He'd also said that the Master-who would not be fooled by the keys-wouldn't hurt them.

Jack personally had his doubts about that one. The Doctor had a problem, he'd noticed, about thinking the best of people, and it absolutely _was_ a _problem_ when it was something that could be written on an autopsy report. On the tiny little off-chance that the Doctor's crazy ex didn't hurt _him_ , there wasn't anything protecting Martha, and she didn't have immortality on her side, either.

That wasn't the kind of oversight Jack was used to seeing from the Doctor, at least this time around. The reckless endangerment tended to stem from legitimate cluelessness, not delusion. He was getting worried about the plan.

He stole a glance at Martha, a few yards and several unsuspecting human beings away. If it came down to it, he decided, he could tackle her from here, cover her with his body. Not exactly ideal circumstances, but…

"Now we know we are not alone," President Winters was saying. "No longer unique in the Universe."

 _Unique_. Ha. That was a trip. Jack could think of thirty alien species off-hand that looked identical to humans. Hell, there were two of them in the room right now.

"And I ask of you now," the President continued, "I ask of the human race, to join me in welcoming our new friends."

Yeah. Yeah, this would go _totally fine_.

Winters held a pause for dramatic effect, looking around the room (his eyes jumping over where they stood beneath their perception filters), and then he flung his arms wide. Triumphantly, he crowed, "I give you the Toclafane!"

Jack had seen this a thousand times; never on this scale, never with Time Lords involved, but the scene itself? A classic. Humans who thought they were controlling some alien power, right up until it turned on them. Advanced species playing human egotism like a fiddle, manipulating them at every angle before throwing them away like yesterday's news. Whether these Toclafane were the players or another set of pawns… well, they'd know for sure once President Winters shut up. But it was the chessmaster Jack was worried about.

He let Winters' blathering over "the planet Earth and its associated moon" fade into the background and looked over at the Doctor. The alien was tense, staring at the Toclafane worriedly. Jack wondered if he'd ever come across them before; in all his days as a Time Agent, he'd never even heard of them, but the Doctor had a thousand years of experience on him. If anybody knew the Toclafane, it'd be him.

"Master is our friend," said one of the Toclafane, with childish glee, and everything kind of went downhill from there.

Jack hated being right sometimes.

The Master wore a charming smile while the Toclafane killed President Winters under his orders, and it wasn't a mask. That was the worst thing about him, really, that he was cheerful and energetic and sincerely happy about all of this. He ordered his guards-and of course they were _his_ guards, of _course_ -into position and they raised their semiautomatics and ordered everyone to stay still.

"Now then!" Master said to the cameras still dutifully recording. "Peoples of the Earth, please attend carefully!"

The Doctor pulled off his perception filter. Martha reached out to stop him, but Jack saw it coming and had already darted forward to hold her back; there was still some fragile hope they might not be noticed, and trying to stop the Doctor's suicidal impulses wouldn't help. Martha didn't have any real protections. The Doctor might have forgotten that, but Jack hadn't. Let him martyr himself for her safety.

So they watched, holding as still as possible, while the Doctor was shoved to his knees by two of the guards. True to form, he never stopped shouting.

" _Doctor_ ," the Master sneered, "we meet at last." And then, "Oh, I do love saying that!"

"Stop this! Stop this right now!"

The Master laughed. "Why should I? You come in here with a half-cocked plan and a few low-level perception filters and you expect to win? Oh, _darling_ ," he said, "it's almost like you _wanted_ to be caught."

The Doctor's body language had all shifted, shoulders turned in, head down, and Jack made a split-second decision before the Master even finished speaking. He shoved Martha behind him, a little harsher than intended, and charged the Master's dais. If there was one thing that Jack Harkness was born for, it was creating a distraction. There was still a chance. The guards were too slow, he noted, too accustomed to Saxon's villain monologues and barked commands. They were out of practice with autonomous action.

But as it turned out, the guards weren't Jack's problem. Saxon-the Master-glanced at him at the tail end of his sentence, flourishing a small metal contraption in one hand, and Jack had just enough time to muse on the possibility of getting frequent-dyer miles in the afterlife as his neurons fired for the last time.

* * *

"Hmph," the Master said dismissively, kicking at the corpse no one else could see. To their credit, the guards were taking it in stride. Martha inched her way towards the body.

"Laser screwdriver," the Master told the Doctor. "Who'd have _sonic_?"

The Doctor's fingers twitched fractionally upwards. The Master threw him a withering look. Martha, kneeling beside Jack and checking his vitals like it mattered, was inordinately thankful he didn't seem to care about her, if he knew she was there at all. He might not; she hadn't attacked him, the perception filter had no reason to fail...

"And the good thing is, he's not dead for long!" the Master said. "I get to kill him again!"

"Master," the Doctor implored, " _please_. Calm down." He sighed, eyes flicking between the Master and the floor. "Look at what you're doing! Just- _stop_. If you could see yourself-"

The Master scoffed. "Do you even remember what you _are_ underneath that shimmer? Your death toll's a hundred times higher than mine. _I'm_ just not pretending to be _human_."

There were a lot of things about that that Martha would have made the Doctor explain in any other situation, but she couldn't afford to bring any attention to herself, and under her hand, Jack's pulse had just started again.

He came back to life with a gasp, unnoticed by the others: the humans drawn away by the perception filters, and the Time Lords too busy with a conversation that seemed to be at least half body language, little twitches and aborted gestures and, god, how well did they _know_ each other?

"It's that sound in your head, Master," the Doctor was saying, head angled downwards and looking up at the Master through his lashes. "The drums. I can help you, I can make them stop!"

"Oh, how to shut you up?" the Master bemoaned, glaring, exasperated, at the ceiling. Looked back at the Doctor. "You're so obsessed with the past," he said, "like you think you'll ever be able to get back to the _good old days_. 'I can help you'," he mimicked, and scoffed. "You can't even help the precious little humans you care about so much; how, exactly, do you think you'd go about helping me?"

"I," the Doctor started, and stopped.

"Exactly," the Master said. "You're _pathetic_. You come in here wearing that broken shimmer like a testament to your ineffectuality, your whole little plan banking on me _caring_ what you  _think_ of me… Spoiler alert, _Theta_ , things change. And any chance of getting back that relationship burnt with Gallifrey." He leveled his screwdriver carelessly at the Doctor's chest. "Exactly how many genocides is that now?"

He didn't get a chance to respond. The laser screwdriver's aim dropped to his hip and flashed again, and in a crackle of static and a burst of sparks, something around the Doctor _rippled_ blue-tinted like a force field dropping and shattered.

"Maybe there is something to be said for the good old days after all," the Master said lightly.

The guards holding the Doctor had flinched back. Without anyone holding him up he had fallen forward to his hands and knees, and the first thing Martha noticed was that his hands were facing backwards.

The second thing she noticed was when he went to push himself upright, his arms folding like an accordion as he crouched and stood. His skin was baking powder white stretched thin over too many joints, lanky arms sticking out far past his shirt cuffs, fingers resting almost at his knees. And there were six of those, long and clawed, and his thumbs were up on the insides of his wrists.

"Doctor," Martha said weakly. "What," she started, but Jack's hand clamped over her mouth before she could finish _are you?_

The Doctor turned towards her. _I'm sorry_ , he mouthed, or she thought he did. His face was only half finished. There was a lower jaw and a pale lower lip, and except for the lack of color it looked human enough. But his skull was all in sloping lines that gave him what only looked like a forehead and nose in profile, and he had no ears or eyes that she could tell, and no upper lip. There were bony protrusions on either side of his head, curving slightly like a satellite dish, and the whole thing was shaded in a pointilistic gradient, hundreds of small, dark divots in his skin which reflected when they were caught in the light.

His facial expression didn't change and Martha wasn't sure it even could. "They _trusted_ me," he said to the Master, like it was a conversation they'd had before. "You didn't have to break it."

"Oh!" the Master said, eyes wide and faux-remorseful. "Did you never tell her about the shimmer? That's unfortunate!" He patted the Doctor on the head, and his textbook-perfect frown twisted and reshaped itself, smoothed into a manic grin as he manhandled the nearest TV camera. "Do excuse me," he said, face to the lens like he was making a home movie. "Little bit of personal business, back in a sec!" and he tilted it back on the tripod, giving the billions of people Martha'd forgotten were watching from home a thrilling view of the panelled ceiling.

God, he could have done that _before_ revealing the creature that the Doctor was. Even if it turned out they'd been working together the whole time, if the Doctor had just been pretending to want to save them, he obviously wasn't comfortable being seen like this.

She told herself she was avoiding looking at him because of the perceived violation, and not at all because the shape of his body and how it moved made her uncomfortable.

Meanwhile, Jack didn't seem to have any qualms. Still sprawled on his back, propping himself up on an elbow to watch the proceedings, breathed a laugh. "Hey, Doc," he said. "So that's what you Time Lords really look like, huh?" He grinned, a glint in his eye Martha recognized, and said, "Y'know, I bet getting head from that mouth'd be an adve-"

Blood splattered on her arms, and the guards lowered their guns halfway again; with a nod from the Master, two of them grabbed the Doctor again, although he was left allowed to stand this time. The Master pulled something out of his suit jacket, one of the guns the Dalek experiments from Manhattan had carried.

"Our, ah… _mutual friends_ at Torchwood One had this beautiful thing in their archives," the Master said. "I thought you would appreciate it." He aimed for the Doctor's chest, raised an eyebrow that presumably didn't actually exist. "Don't worry, it won't do permanent damage. Or, well, much of it."

The Doctor screamed for a very long time. It was shrill and glotallized staticky-sounding, like bad radio reception, and it never wavered even when he definitely should have needed to breathe, or when he stopped thrashing and just hung there. Eventually the Master took his finger off the trigger, and the guards let him drop to the floor like dead weight. He laid there shivering and twitching and doing something with his chest that might have been panting, and the Master closed his eyes and smiled, basking in the sound of the Doctor's pain.

Martha stared. She wanted to run to him, to help him somehow-check for shock or concussion, offer emotional support, to do _something_ other than sit there and watch-but some animal instinct kept her rooted in place. _You can't trust it_ , it whispered, _it's dangerous, it's alien, it doesn't count. Protect yourself instead_ , it told her, and she didn't- _couldn't_ move.

"You're beautiful," Lucy Saxon breathed. The Doctor shifted to look up at her, and somehow that was enough to make Martha resolve herself. Maybe the desperation in the movement, maybe just needing to be better than _Lucy Saxon_ , but she shoved her instincts back in her hindbrain where they belonged and slipped carefully to the Doctor's side, taking hold of his hand.

He was still shaking, making pained noises in the back of his throat and jerking involuntarily, but he gripped tightly to her hand. "Martha," he whispered, "the Archangel Network."

"I know, Doctor," she reassured, trailing a hand down his-well, she supposed it was part of his face. She wasn't sure how to check for concussion in someone who didn't have eyes, but he was definitely confused. "It's how he got everyone to vote for-"

"No," the Doctor said. "Archangel, it's-it's a telepathic network. It works both ways, picks up on what the whole planet is thinking. If they're afraid, that's what spreads, but if you give them _hope_ …"

Somewhere in the background the Master was grandstanding again, but Martha wasn't listening.

"You have to give them hope, Martha," the Doctor said. And after another violent muscle spasm, "The perception filter will hide you. If you get them to believe they're protected, they can make it real. The Master isn't immortal."

"How am I supposed to give them _hope_?" she asked.

"I-I'd say tell them I'll save them, but that'd be a bit of a tall order now, I think." His mouth twitched, and she realized he was smiling. "You'll figure it out, I'm sure. There's no one I'd rather put the fate of the world in the hands of."

She killed a potplant her first year of university. Now the Doctor was expecting her to keep the whole world alive?

"People are a little more self sufficient than potplants," the Doctor said.

Martha jerked back.

"Oh. Oh, I'm sorry," he said, "I didn't mean to listen in. Having trouble telling what's words and what isn't. Won't happen again, I promise."

"You _read minds_?" she hissed.

"I-"

"Ah, Martha Jones!" the Master interrupted, as if he'd just noticed her. "Hello again! I _do_ hope you don't think I've _forgotten_ about you!" He smiled. "In fact, to make you feel at home, I've brought you...something of a gift. I hope you don't mind. We've flown them in all the way from prison!" He gestured ornately, a sweep like an old-time circus ringmaster, and the door opened, Martha's parents and sister marched in, flanked by more of the Master's guards.

God. Whatever _else_ he was, Martha told herself, no matter what he'd hidden from her, he was still the Doctor, and she had to trust him. She didn't have any other choice. She disentangled herself as gently as she could, and stood. "Mum," she said.

"I'm sorry."

"It's not your fault!" Martha said, and gave her the second cousin of a smile. She couldn't leave them to the Master. She could barely let herself leave Jack and the Doctor as it was, and they could handle themselves; she had no idea if her family could. She had to put them first.

The Master stalked towards her and Martha flinched back, but he didn't so much as look at her. He grabbed the Doctor's upper arm roughly, pulling him up and probably dislocating the Doctor's shoulder in the process, until he had the Doctor pressed up against him, the Master almost entirely holding up his weight. He kept the bruising grip on the Doctor's arm, and his other hand was at his jaw, forcing the Doctor to look out the window at the Toclafane.

"Do you know what they are, Theta?" the Master said.

The Doctor flinched.

"I made them special for you," he said, low enough that the Doctor and Martha, a few feet away, could hear. "You were right, you know. Humans are so _adaptable_."

" _No_!" the Doctor said, and struggled in his grip. The Master's hand moved up from his arm to the crook of his shoulder, and he went still. "Why would you-" the Doctor said, unmoving as the Master mouthed at his neck beneath the base of the bony protrusion of his skull. "What did they do to deserve that?"

The Master suddenly pushed the Doctor away from him, and he caught himself almost at Martha's feet. His neck was already bruising sinopia.

"They _asked_ me to do it," the Master crowed, "I only gave them what they wanted! I _helped_ them! They were so _lost_ and _alone_ , so I saved them, and, oh, how do you put it? _Showed them the stars_. Don't you approve?"

Jack revived with a gasp, then closed his eyes and laid perfectly still. The Master, twirling his wife with a joyous sort of madness, didn't notice him, and Martha wished she could be so lucky.

"How many, do you think?" the Master said to Lucy, who giggled and demured. And then, "Six billion, all at the end of the Universe where no one would miss them!" He pulled away from his wife and turned back to the Doctor, as if there'd never been an interruption. "And after I saved them, I promised my new children… this." He spread his arms wide, rapturously, a twisted savior figure. "That we would desecrate and decimate this _pathetic_ planet!"

The Doctor wasn't the only one who flinched then, but the Master's voice was measured when he spoke again. "Good word, 'decimate'. Know what it means, Theta?"

"No, no, you _can't_ -"

"Kids!" the Master called. "Remove one tenth of the population!"

Martha raised a half-formed fist to her mouth, watching helplessly as, out the window, the Toclafane surged towards the surface. The Master flipped on some comms system and the Valiant's radios becan crackling desperately, drowning out the frantic transmissions, _Valiant, this is-_

_-getting slaughte-_

_-liant, report-_

_-for God's sa-_

_-'re dying!_ and the Master laughed, twirling Lucy again before going back around to the forgotten camera. He tilted the lens back down.

"Hello, Earthlings! Any of you still watching this and _not_ running around like ants… You seem to have missed an important memo. Basically: end of the world." He shrugged, like _silly old me_.

"You're sick," Martha's mother spat, struggling in the guards' grips.

The Master turned to her, raising an eyebrow. "I'm your Master," he said, "and you will obey me." Spinning on his heel and narrowing his eyes: " _Won't she_ , Martha Jones?"

Martha opened her mouth, whether to say _just listen to him, Mum_ or shout her defiance she didn't know. But whatever it was, she never had the chance. Jack stood and lunged, tackling her to the floor. She felt something clasp around her wrist and for half a second all she could think was _no, he can't be a traitor, it's not fair!_ before Jack pushed himself off of her again, blocking her, she realized, from the Master's view. She looked down to see what he had done and barely had time to recognize the device befor its auto-jump feature lit up LED-green.

"No, I can't just-"

She had the sense of being pulled apart, of being shoved into a gaping space of dead memory, of atoms wandering hither and thither, far-away from sentient-movement, and she tumbled head over nonexistent heels as Hampstead rushed up to meet her.

"-leave them!"

She pulled herself to her feet, slowly regaining a bearing on physical form. London was burning. The Toclafane poured in from a tear in the sky, a long line of them stretched out overhead like worker ants. She tensed to run, but they didn't see her. They weren't Time Lords.

Martha ran shaking fingers over the metal of the _Tardis_ key, and thought, _thank you_. Even as that shattered, cannibalized hulk of a thing, she was able to protect her.

"I'll come back," she said to no one. "When I'm finished."

There was screaming from London, and she could hear it from here. Martha Jones steeled herself, turned her back, and walked away.

**Author's Note:**

> Sorry for quoting Dryden and Titus Lucretius, but in my defense I'm a fucking pretentious piece of shit.
> 
> "And All the Wandering Motions" is a project that me and Jo @mylordshesacactus did together back in 2013 for NaNo. As it was for NaNo and also from several years back, I'm...less than thrilled with certain technical aspects of the prose. However, I'm not a huge fan of just editing something that's already out there without in some way building on the content or taking a different approach to it. Luckily, I'm in the middle of working on my thesis, and I really need a break from working on my thesis. Jo has respectfully bowed out of involvement this time around, and I don't blame her.
> 
> Please be patient with the update schedule-namely, that one does not exist-and if you take it upon yourself to read AATWM, please don't judge us too hard.
> 
> On certain aspects of the writing:  
> 1) I chose to use the form _Tardis_ because a) that is what is used in early scripts, memos, articles, etc, and I am a crotchety old Classic Whovian, and b) it feels more like a name to me, that way, and the _Tardis_ is absolutely a character in her own right.  
>  2) For simplicity's sake, we're assuming here a canon timeline of Dr.Who (1963) -> Virgin New Adventures -> Dr.Who (1996) -> Eighth Doctor Adventures -> Dr.Who (2005) -> Sarah Jane Adventures, featuring a few references to some obscure DWM shorts and comics. I'm ignoring Torchwood, Shalka is an alternate worldline, the only Big Finish referenced is a slight AU of "Master" and some spec bio from "Scherzo". Except as outlined, everything is 100% canon compliant. [That's](http://transgirlsamwinchester.tumblr.com/post/112244458700) [kind](http://transgirlsamwinchester.tumblr.com/post/107245416740) [of](http://transgirlsamwinchester.tumblr.com/post/109073371810) [my](http://transgirlsamwinchester.tumblr.com/post/112807683250) [thing](http://transgirlsamwinchester.tumblr.com/post/81971963986). There's more canon to say that Gallifreyans don't look human, even considering that "humans look Time Lord" shit that necessarily only means Gallifreyans are bipedal, and basically every biological process mentioned has basis in canon. I can and will show my work.  
> 3) Names and pronouns used to refer to everybody's fave canonically trans murder alien vary due to POV and also what language is happening at the moment (more on that later). Word of God here to clarify that 10's pronouns are he/him/his and 11's pronouns are ey/em/eir.


End file.
